Summary: The highly pathogenic SHIVDH12R rhesus macaque animal model system was used to evaluate a vaccine regimen, which presents the HIV-1 envelope in its most native form: as a component of intact virions. Aldrithiol-2 (AT-2) inactivated particles were administered to boost immune responses initially primed with a mixture of recombinant vaccinia viruses expressing SIV Gag and Pol proteins and HIV-1 Env. AT-2 was used for inactivation since previous studies had shown that this treatment preserved the native structure and function of virion-associated envelope proteins. Inactivated SIV particles were also included in the immunization mix to elicit immune responses against several other viral proteins (viz. Gag and Pol). Following challenge with the closely related but heterologous (relative to the HIV-1 Env antigens) SHIVDH12R-PS1, vaccinated animals readily controlled virus infection and SHIV-induced depletion of CD4+ T lymphocytes. CD8+ T cell and neutralizing Ab responses were detected following challenge suggesting that cellular and humoral immunity contributed to the protection conferred by the vaccine regimen. Despite the control of SHIV-induced disease, replication competent virus was isolated from all four vaccinated animals 22 weeks post-challenge. The virus recovered from the vaccinated monkey with the lowest set point viremia caused a rapid and irreversible loss of CD4+ T cells following inoculation into a naive animal. These results demonstrate that an ongoing infection by a highly pathogenic SHIV was being controlled by the immune system in the vaccinated rhesus macaques.